Gramene release # 56b: updates to Plant Reactome

In Gramene release 56b, we present recent updates of Plant Reactome, the pathway portal of Gramene. We have added 22 newly curated pathways, 3 updated pathways, 8 newly projected species, and gene interaction data to Plant Reactome. The Plant Reactome database was built in collaboration with the Reactome project.

Pathway Curation

This release contains 22 newly curated and 3 revised pathways from reference species rice (O. sativa). The hierarchical list of pathways has been updated accordingly.

Newly curated pathways:

• Reproductive structure development
• Anther and pollen Development
• Vegetative structure development
• Primary root development
• Response to submergence
• Underwater shoot and internode elongation
• Response to phosphate deficiency
• Photorespiration
• Ureide biosynthesis
• Beta-alanine betaine biosynthesis
• Proline biosynthesis V from arginine
• Phospholipid biosynthesis I
• Sphingolipid metabolism
• Response to iron deficiency
• Mugineic acid biosynthesis
• Iron uptake and transport in root vascular system
• Proline degradation
• Glutamate degradation
• Phenylalanine degradation III
• Lysine degradation II
• Threonine degradation

Revised pathways:

• Cardiolipin biosynthesis
• Ent-kaurene biosynthesis
• Responses to stimuli

Pathway Projections (8 new species included)

The Plant Reactome has expanded gene homology-based pathway projections to 74 plant species. Newly projected species include garden cucumber (Cucumis sativus), white yam (Dioscorea rotundata), sunflower (Helianthus annuus), white jute (Corchorus capsularis), blue lupin (Lupinus angustifolius), coyote tobacco (Nicotiana attenuata), Irish moss (Chondrus crispus), and an extremophilic unicellular species of red algae Galdieria sulphuraria (capable of photosynthesis as well as heterotrophic growth by utilizing ~50 different extracellular carbon sources).

In addition, we have revised pathway projections (converted from Inparanoid to Compara orthology) for three species: a wild South American cotton (Gossypium raimondii), cassava (Manihot esculenta), and common bean (Phaseolus vulgaris). Notable updated Compara orthology data has been kindly provided by Ensembl for updated species.

Pathway Projection Statistics and Status (update/new)

• *data from sequenced transcriptomes
• ^ projections currently exclude cell-cycle pathways and annotations
• Planteome Inparanoid data was kindly provided by the Planteome project
• When available the outgoing links from gene product IDs mapped to reactions are always hyperlinked to respective entries in collaborator databases/online resources

NOTE: The pathway counts for both reference and projected species include a few organizational “container” names, such as “Hormone biosyntheses” and “Metabolism”. Additionally, the bulk of the projected pathways occur in the areas of metabolic and regulatory function, whereas the rice reference data set has additional pathways related to cell cycle functions. We are not currently using these additional pathways as a source for orthology projection. Visit the Download page to access the updated data files associated with pathways, reactions, gene products, metabolites and external reference sources such as ChEBI, Ensembl, and UniProt.

New Functionalities: 

Expanded Reference Species Gene Name listings

Additional and alternate O. sativa gene names are now visible under the Molecules tab when viewing rice pathways.

Interactor Overlays

Users can display gene-gene interaction data on Plant Reactome pathways either by choosing a publicly-available dataset under “Interactor Overlay”, or by uploading a dataset of their choice. This feature can aid researchers by extending the network of known complexes and pathways with candidate proteins. The Plant Reactome team has specifically provided locally-hosted interaction data for A. thaliana (courtesy of the Planteome project). This data can be viewed by selecting “Plant Interactome” on the Interactor Overlay panel and A. thaliana on the species selector.